Characterizing the distribution of an endangered salmonid using environmental DNA analysis
Summary
Determining species distributions accurately is crucial to developing conservation and management strategies for imperiled species, but a challenging task for small populations. We evaluated the efficacy of environmental DNA (eDNA) analysis for improving detection and thus potentially refining the known distribution of Chinook salmon (Oncorhynchus tshawytscha) in the Methow and Okanogan Subbasins of the Upper Columbia River, which span the border between Washington, USA and British Columbia, Canada. We developed an assay to target a 90 base pair sequence of Chinook DNA and used quantitative polymerase chain reaction (qPCR) to quantify the amount of Chinook eDNA in triplicate 1-L water samples collected at 48 stream locations in June [...]
Summary
Determining species distributions accurately is crucial to developing conservation and management
strategies for imperiled species, but a challenging task for small populations. We evaluated the efficacy
of environmental DNA (eDNA) analysis for improving detection and thus potentially refining the known
distribution of Chinook salmon (Oncorhynchus tshawytscha) in the Methow and Okanogan Subbasins of
the Upper Columbia River, which span the border between Washington, USA and British Columbia, Canada.
We developed an assay to target a 90 base pair sequence of Chinook DNA and used quantitative polymerase
chain reaction (qPCR) to quantify the amount of Chinook eDNA in triplicate 1-L water samples
collected at 48 stream locations in June and again in August 2012. The overall probability of detecting
Chinook with our eDNA method in areas within the known distribution was 0.77 (±0.05 SE). Detection
probability was lower in June (0.62, ±0.08 SE) during high flows and at the beginning of spring Chinook
migration than during base flows in August (0.93, ±0.04 SE). In the Methow subbasin, mean eDNA concentration
was higher in August compared to June, especially in smaller tributaries, probably resulting
from the arrival of spring Chinook adults, reduced discharge, or both. Chinook eDNA concentrations
did not appear to change in the Okanogan subbasin from June to August. Contrary to our expectations
about downstream eDNA accumulation, Chinook eDNA did not decrease in concentration in upstream
reaches (0–120 km). Further examination of factors influencing spatial distribution of eDNA in lotic systems
may allow for greater inference of local population densities along stream networks or watersheds.
These results demonstrate the potential effectiveness of eDNA detection methods for determining landscape-
level distribution of anadromous salmonids in large river systems.
